def next(self):
"""Returns the data from the call to the GenomicsAPI
Raises:
StopIteration: The data has been exhausted.
"""
# If it's your first time or you have a token then make the call.
if self._firstTime or self._nextPageToken:
api = GenomicsAPI()
# Get the results
try:
content = api.read_search(self._readsetId, self._sequenceName,
self._sequenceStart,
self._sequenceEnd,
self._nextPageToken)
self._firstTime = False
except ApiException as exception:
logging.warning("API exception: %s" % exception.message)
raise StopIteration()
self._nextPageToken = content[
"nextPageToken"] if 'nextPageToken' in content else None
return content, self._sequenceStart, self._sequenceEnd
else:
raise StopIteration()
def next(self):
"""Returns the data from the call to the GenomicsAPI
Raises:
StopIteration: The list of files has been exhausted.
"""
# If it's your first time or you have a token then make the call.
if self._firstTime or self._nextPageToken:
api = GenomicsAPI()
# Get the results
content = None
try:
content = api.read_search(self._readsetId, self._sequenceName,
self._sequenceStart, self._sequenceEnd,
self._nextPageToken)
self._firstTime = False
except ApiException as exception:
errorMessage = exception.message
raise StopIteration()
self._nextPageToken = content["nextPageToken"] if 'nextPageToken' in content else None
return (content, self._sequenceStart, self._sequenceEnd)
else:
# All Done
#logging.debug("GenomicsAPIInputReader next() is Done start: %d end: %d.",
# self._sequenceStart, self._sequenceEnd)
raise StopIteration()
def generate_coverage_map(data):
"""Generate coverage map function."""
(content, sequenceStart, sequenceEnd) = data
reads = content['reads'] if 'reads' in content else []
coverage = GenomicsAPI.compute_coverage(reads, sequenceStart,
sequenceEnd)
for key, value in coverage.iteritems():
yield (key, value)
def generate_coverage_map(data):
"""Generate coverage map function."""
(content, sequenceStart, sequenceEnd) = data
if content is not None and 'reads' in content:
coverage = GenomicsAPI.compute_coverage(content['reads'],
sequenceStart, sequenceEnd)
for key, value in coverage.iteritems():
yield (key, value)
def generate_coverage_map(data):
"""Generate coverage map function."""
(content, sequenceStart, sequenceEnd) = data
reads = content['reads'] if 'reads' in content else []
coverage = GenomicsAPI.compute_coverage(reads, sequenceStart,
sequenceEnd)
for key, value in coverage.iteritems():
yield (key, value)
def next(self):
"""Returns the data from the call to the GenomicsAPI
Raises:
StopIteration: The data has been exhausted.
"""
# If it's your first time or you have a token then make the call.
if self._firstTime or self._nextPageToken:
api = GenomicsAPI()
# Get the results
try:
content = api.read_search(self._readsetId, self._sequenceName,
self._sequenceStart, self._sequenceEnd,
self._nextPageToken)
self._firstTime = False
except ApiException as exception:
logging.warning("API exception: %s" % exception.message)
raise StopIteration()
self._nextPageToken = content["nextPageToken"] if 'nextPageToken' in content else None
return content, self._sequenceStart, self._sequenceEnd
else:
raise StopIteration()
def next(self):
"""Returns the data from the call to the GenomicsAPI
Raises:
StopIteration: The list of files has been exhausted.
"""
# If it's your first time or you have a tokent then make the call.
if self._firstTime or self._nextPageToken:
# Determine if we are using the real or mock Genomics API.
api = MockGenomicsAPI() if self._useMockData else GenomicsAPI()
# Get the results
try:
content = api.read_search(self._readsetId, self._sequenceName,
self._sequenceStart,
self._sequenceEnd,
self._nextPageToken)
self._firstTime = False
except ApiException as exception:
errorMessage = exception.message
# TODO not sure what we do here if we can't get content?
raise StopIteration()
if content is not None:
if 'nextPageToken' in content:
self._nextPageToken = content["nextPageToken"]
if 'reads' in content:
return (content, self._sequenceStart, self._sequenceEnd)
else:
# TODO not sure what we do here if we got content but not as expected?
raise StopIteration()
else:
# All Done
logging.debug("GenomicsAPIInputReader next() is Done "
"start: %d end: %d." %
(self._sequenceStart, self._sequenceEnd))
raise StopIteration()
def post(self):
# Collect inputs.
readsetId = self.request.get("readsetId")
sequenceName = self.request.get('sequenceName')
sequenceStart = int(self.request.get('sequenceStart'))
sequenceEnd = int(self.request.get('sequenceEnd'))
useMockData = self.request.get('useMockData')
# TODO: Validate inputs such as sequence start and end to make
# sure they are in bounds based on TARGETS.
content = None
coverage = None
errorMessage = None
if self.request.get("submitRead"):
# Use the API to get the requested data.
# If you are running the real pipeline map reduce then hit it.
if self.request.get('runPipeline'):
logging.debug("Running pipeline")
pipeline = CoveragePipeline(readsetId, sequenceName,
sequenceStart, sequenceEnd,
useMockData)
pipeline.start()
self.redirect(pipeline.base_path + "/status?root=" +
pipeline.pipeline_id)
return
if useMockData:
# Use the mock to get coverage information.
mock = MockGenomicsAPI()
content = mock.read_search(readsetId, sequenceName,
sequenceStart, sequenceEnd)
else:
# Make the API call here to process directly.
try:
api = GenomicsAPI()
content = api.read_search(readsetId, sequenceName,
sequenceStart, sequenceEnd)
except ApiException as exception:
errorMessage = exception.message
elif self.request.get("submitReadSample"):
# Read in local sample data which is based off of default settings.
body = MainHandler.DEFAULT_SETTINGS
path = os.path.join(
os.path.split(__file__)[0], 'static/listRead_SampleData.json')
file = open(path, 'r')
content = file.read()
file.close()
content = json.loads(content)
# If you have content then compute and store the results.
if content is not None:
if 'reads' in content:
# Calculate results
coverage = compute_coverage(content, sequenceStart,
sequenceEnd)
# TODO make a setting to turn this on/off?
#store_coverage(readsetId, sequenceName, coverage)
else:
errorMessage = "There API did not return any reads to process."
else:
errorMessage = "No content was returned to process."
# Render template with results or error.
username = users.User().nickname()
template = JINJA_ENVIRONMENT.get_template('index.html')
self.response.out.write(
template.render({
"username": username,
"targets": MainHandler.TARGETS,
"settings": {
'readsetId': readsetId,
'sequenceName': sequenceName,
'sequenceStart': sequenceStart,
'sequenceEnd': sequenceEnd,
'useMockData': useMockData,
},
"errorMessage": errorMessage,
"results": coverage,
}))
def post(self):
# Collect inputs.
readsetId = self.request.get("readsetId")
sequenceName = self.request.get('sequenceName')
sequenceStart = int(self.request.get('sequenceStart'))
sequenceEnd = int(self.request.get('sequenceEnd'))
useMockData = self.request.get('useMockData')
# TODO: Validate inputs such as sequence start and end to make
# sure they are in bounds based on TARGETS.
reads = []
coverage = None
errorMessage = None
if self.request.get("submitRead"):
# Use the API to get the requested data.
# If you are running the real pipeline map reduce then hit it.
if self.request.get('runPipeline'):
logging.debug("Running pipeline")
pipeline = PipelineGenerateCoverage(readsetId, sequenceName,
sequenceStart, sequenceEnd,
useMockData)
pipeline.start()
self.redirect(pipeline.base_path + "/status?root=" +
pipeline.pipeline_id)
return
# Make the API calls directly from the web ui.
api = GenomicsAPI()
# Use the Mock API if requested.
if useMockData:
api = MockGenomicsAPI()
# Make the call.
try:
pageToken = None
firstTime = True
while firstTime or pageToken is not None:
content = api.read_search(readsetId, sequenceName,
sequenceStart, sequenceEnd,
pageToken)
firstTime = False
if 'reads' in content:
reads += content['reads']
pageToken = content['nextPageToken'] if 'nextPageToken' in content\
else None
except ApiException as exception:
errorMessage = exception.message
elif self.request.get("submitReadSample"):
# Read in local sample data which is based off of default settings.
readsetId = MainHandler.DEFAULT_SETTINGS['readsetId']
sequenceName = MainHandler.DEFAULT_SETTINGS['sequenceName']
sequenceStart = MainHandler.DEFAULT_SETTINGS['sequenceStart']
sequenceEnd = MainHandler.DEFAULT_SETTINGS['sequenceEnd']
path = os.path.join(
os.path.split(__file__)[0], 'static/listRead_SampleData.json')
file = open(path, 'r')
content = file.read()
file.close()
content = json.loads(content)
reads = content['reads']
# If you have content then compute and store the results.
if reads is not None and len(reads) > 0:
# Calculate results
coverage = GenomicsAPI.compute_coverage(reads, sequenceStart,
sequenceEnd)
# TODO make a setting to turn this on/off?
#GenomicsCoverageStatistics.store_coverage(readsetId, sequenceName,
# coverage)
else:
errorMessage = "There API did not return any reads to process."
# Render template with results or error.
username = users.User().nickname()
version = os.environ['CURRENT_VERSION_ID']
template = JINJA_ENVIRONMENT.get_template('index.html')
self.response.out.write(
template.render({
"username": username,
"version": version,
"targets": GenomicsAPI.TARGETS,
"settings": {
'readsetId': readsetId,
'sequenceName': sequenceName,
'sequenceStart': sequenceStart,
'sequenceEnd': sequenceEnd,
'useMockData': useMockData,
},
"errorMessage": errorMessage,
"results": coverage,
}))
def post(self):
# Collect inputs.
readsetId = self.request.get("readsetId")
sequenceName = self.request.get('sequenceName')
sequenceStart = int(self.request.get('sequenceStart'))
sequenceEnd = int(self.request.get('sequenceEnd'))
useMockData = self.request.get('useMockData')
# TODO: Validate inputs such as sequence start and end to make
# sure they are in bounds based on TARGETS.
reads = []
coverage = None
errorMessage = None
if self.request.get("submitRead"):
# Use the API to get the requested data.
# If you are running the real pipeline map reduce then hit it.
if self.request.get('runPipeline'):
pipeline = PipelineGenerateCoverage(readsetId, sequenceName,
sequenceStart, sequenceEnd,
useMockData)
pipeline.start()
self.redirect(pipeline.base_path + "/status?root="
+ pipeline.pipeline_id)
return
# Make the API calls directly from the web ui.
api = GenomicsAPI()
# Use the Mock API if requested.
if useMockData:
api = MockGenomicsAPI()
# Make the call.
try:
pageToken = None
firstTime = True
while firstTime or pageToken is not None:
content = api.read_search(readsetId, sequenceName, sequenceStart,
sequenceEnd, pageToken)
firstTime = False
if 'reads' in content:
reads += content['reads']
pageToken = content['nextPageToken'] if 'nextPageToken' in content\
else None
except ApiException as exception:
errorMessage = exception.message
elif self.request.get("submitReadSample"):
# Read in local sample data which is based off of default settings.
readsetId = MainHandler.DEFAULT_SETTINGS['readsetId']
sequenceName = MainHandler.DEFAULT_SETTINGS['sequenceName']
sequenceStart = MainHandler.DEFAULT_SETTINGS['sequenceStart']
sequenceEnd = MainHandler.DEFAULT_SETTINGS['sequenceEnd']
path = os.path.join(os.path.split(__file__)[0],
'static/reads-search_sample_data.json')
file = open(path, 'r')
content = file.read()
file.close()
content = json.loads(content)
reads = content['reads']
# Calculate results
coverage = GenomicsAPI.compute_coverage(reads, sequenceStart, sequenceEnd)
# TODO make a setting to turn this on/off?
#GenomicsCoverageStatistics.store_coverage(readsetId, sequenceName,
# coverage)
# Render template with results or error.
username = users.User().nickname()
template = JINJA_ENVIRONMENT.get_template('index.html')
self.response.out.write(template.render({
"username": username,
"version": self._get_version(),
"targets": GenomicsAPI.TARGETS,
"settings": {
'readsetId': readsetId,
'sequenceName': sequenceName,
'sequenceStart': sequenceStart,
'sequenceEnd': sequenceEnd,
'useMockData': useMockData,
},
"errorMessage": errorMessage,
"results": coverage,
}))
def post(self):
# Collect inputs.
readsetId = self.request.get("readsetId")
sequenceName = self.request.get('sequenceName')
sequenceStart = int(self.request.get('sequenceStart'))
sequenceEnd = int(self.request.get('sequenceEnd'))
useMockData = self.request.get('useMockData')
# TODO: Validate inputs such as sequence start and end to make
# sure they are in bounds based on TARGETS.
content = None
coverage = None
errorMessage = None
if self.request.get("submitRead"):
# Use the API to get the requested data.
# If you are running the real pipeline map reduce then hit it.
if self.request.get('runPipeline'):
logging.debug("Running pipeline")
pipeline = CoveragePipeline(readsetId, sequenceName, sequenceStart,
sequenceEnd, useMockData)
pipeline.start()
self.redirect(pipeline.base_path + "/status?root="
+ pipeline.pipeline_id)
return
if useMockData:
# Use the mock to get coverage information.
mock = MockGenomicsAPI()
content = mock.read_search(readsetId, sequenceName, sequenceStart,
sequenceEnd)
else:
# Make the API call here to process directly.
try:
api = GenomicsAPI()
content = api.read_search(readsetId, sequenceName, sequenceStart,
sequenceEnd)
except ApiException as exception:
errorMessage = exception.message
elif self.request.get("submitReadSample"):
# Read in local sample data which is based off of default settings.
body = MainHandler.DEFAULT_SETTINGS
path = os.path.join(os.path.split(__file__)[0],
'static/listRead_SampleData.json')
file = open(path, 'r')
content = file.read()
file.close()
content = json.loads(content)
# If you have content then compute and store the results.
if content is not None:
if 'reads' in content:
# Calculate results
coverage = compute_coverage(content, sequenceStart, sequenceEnd)
# TODO make a setting to turn this on/off?
#store_coverage(readsetId, sequenceName, coverage)
else:
errorMessage = "There API did not return any reads to process."
else:
errorMessage = "No content was returned to process."
# Render template with results or error.
username = users.User().nickname()
template = JINJA_ENVIRONMENT.get_template('index.html')
self.response.out.write(template.render({
"username": username,
"targets": MainHandler.TARGETS,
"settings": {
'readsetId': readsetId,
'sequenceName': sequenceName,
'sequenceStart': sequenceStart,
'sequenceEnd': sequenceEnd,
'useMockData': useMockData,
},
"errorMessage": errorMessage,
"results": coverage,
}))
